Find research datasets worth reusing

opencc-by-4.0Dec 2011View details →

Fig. 2. Sepia acuminata, lectotype NHMUK 1890.9.22.332 in Primary types in the collection of molluscs in the KwaZulu-Natal Museum: Scaphopoda and Cephalopoda

Fig. 2. Sepia acuminata, lectotype NHMUK 1890.9.22.332 (102×37 mm).

opencc-by-4.0Dec 2011View details →

Fig. 1. Dentalium regulare, syntype NMSA 2575 in Primary types in the collection of molluscs in the KwaZulu-Natal Museum: Scaphopoda and Cephalopoda

Fig. 1. Dentalium regulare, syntype NMSA 2575/T687, 25.2×4.0 mm.

opencc-zeroMay 2023View details →

Data from: Integrating multiple sign types to improve occupancy estimation for inconspicuous species

Standard occupancy models enable unbiased estimation of occupancy by accounting for observation errors such as missed detections (false negatives) and, less commonly, incorrect detections (false positives). Occupancy models are fitted to data from repeated site visits in which surveyors record evidence of species presence. Use of indirect sign (e.g., scat, tracks) as evidence of presence can vastly improve survey efficiency for inconspicuous species but can also introduce additional sources of error. We developed a "multi‐sign" occupancy approach to model the detection process separately for unique sign types and used this method to improve estimates of occupancy dynamics for an inconspicuous species, the American pika (Ochotona princeps). We investigated how estimates of pika occupancy and environmental drivers differed under four increasingly realistic representations of the observation process: (1) perfect detection (commonly assumed for modeling pika occupancy), (2) standard occupancy model (single observation process without possibility of false detection), (3) multi‐sign with no false detections (non‐false positive model), and (4) multi‐sign with false detections (full model). For the multi‐sign occupancy models, we modeled the detection of each sign type (fresh scat, fresh haypiles, pika calls, and pika sightings) separately as a function of climatic and environmental covariates. Estimates of occupancy processes and inferences about environmental drivers were sensitive to different detection models. Simplified representations of the detection processes generally resulted in higher occupancy estimates and higher turnover rates than the full multi‐sign model. Environmental drivers also varied in their influence on occupancy models, where (e.g.) forb cover was estimated to more strongly influence occupancy in the full multi‐sign model than the simpler models. As has been reported previously in other contexts, unmodeled heterogeneity in the observation process can lead to biases in occupancy processes and uncertainty in the relationships between occupancy and environmental covariates. Overall, our multi‐sign approach to dynamic occupancy modeling, which accounts for spatiotemporal variation in reliability among sign types, has strong potential to generate more realistic estimates of occupancy dynamics for inconspicuous species.

opencc-by-4.0May 2023View details →

Data sets from "How amenable is type 2 diabetes treatment for precision diabetology? A meta-regression of glycaemic control data from 174 randomised trials"

The two data sets (in CSV format) contain the complete infomation to reproduce the analyses from the paper "How amenable is type 2 diabetes treatment for precision diabetology? A meta-regression of glycaemic control data from 174 randomised trials" which will be published in Diabetologia. The data set "Data_LogSD.csv" contains the data for the primary analysis of the Log(SD) as given in the main paper, the data set "Data_LogSD_BL_CORR.csv" contains the data for the analysis of the baseline-corrected Log(SD) as given in the electronic supplementary material.

opencc-by-4.0May 2023View details →

Additional raw data in `Cell-type-specific co-expression inference from single cell RNA-sequencing data'.

This repository holds the additional raw data used to generate figures in the publication "Cell-type-specific co-expression inference from single cell RNA-sequencing data" (preprint version: <a href="http://source%20code%20repo%20for%20%60cell-type-specific%20co-expression%20inference%20from%20single%20cell%20rna-sequencing%20data%27./">https://www.biorxiv.org/content/10.1101/2022.12.13.520181v1</a>). Table of contents: <ul> <li>Figure_1B.rds:  <ul> <li>raw data of Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_1B.rds:  <ul> <li>raw data of Supplementary Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_2.rds:  <ul> <li>raw data of Supplementary Figure 2 </li> <li>empirical power evaluated for 4999 gene pairs and 6 methods</li> </ul> </li> <li>Figure_3B.rds:  <ul> <li>raw data of Figure 3B</li> <li>co-expression estimates of a network of 500 genes for 9 methods across 100 replicates</li> </ul> </li> <li>Additional_Raw_Data.xlsx <ul> <li>raw data of Figure 3A: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods</li> <li>raw data of Figure 3C: running times for 11 methods</li> <li>raw data of Supplementary Figure 3: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods under two settings of sequencing detph variations</li> </ul> </li> </ul>

opencc-by-4.0Jun 2023View details →

GEO-Bench: m-SA-crop-type

GEO-Bench: m-SA-crop-type dataset This dataset has been modified to be included in the <a href="https://zenodo.org/communities/geo-bench/">GEO-Bench dataset</a>. All changes with respect to the original version are documented at <a href="https://github.com/ServiceNow/geo-bench">https://github.com/ServiceNow/geo-bench</a>. The original version of this dataset is due to the Western Cape Department of Agriculture and the Radiant Earth Foundation (2021) and is available at: <a href="https://mlhub.earth/data/ref_south_africa_crops_competition_v1">https://mlhub.earth/data/ref_south_africa_crops_competition_v1</a>. See the LICENSE file provided alongside this dataset for applicable licensing information.

opencc-zeroJun 2023View details →

Geography, environment, and colonization history interact with morph type to shape genomic variation in an Arctic fish

Polymorphic species are useful models for investigating the evolutionary processes driving diversification. Such processes include colonization history as well as contemporary selection, gene flow, and genetic drift, which can vary between intraspecific morphs as a function of their distinct life histories. The interactive and relative influence of such evolutionary processes on morph differentiation critically informs morph-specific management decisions and our understanding of incipient speciation. We therefore investigated how geographic distance, environmental conditions, and colonization history interacted with morph migratory capacity in the highly polymorphic fish species, Arctic Charr (Salvelinus alpinus). Using an 87k SNP chip we genetically characterized recently evolved anadromous, resident, and landlocked charr collected from 45 locations across a secondary contact zone of three charr glacial lineages in eastern Canada. A strong pattern of isolation by distance across all populations suggested geographic distance principally shaped genetic structure. Landlocked populations had lower genetic diversities and higher genetic differentiation than anadromous populations. However, genetic diversity was generally temporally stable in landlocked populations in comparison to recent decreases in anadromous populations. Genetic diversity positively correlated with latitude, potentially indicating southern anadromous populations' vulnerability to climate change and greater introgression between the Arctic and Atlantic glacial lineages in northern Labrador. Local adaptation was suggested by the observation of several environmental variables strongly associating with functionally relevant outlier genes including a region on chromosome AC21 potentially associated with anadromy. Our results demonstrate that gene flow, colonization history, and local adaptation uniquely interact to influence the genetic variation and evolutionary trajectory of populations.

openJun 2023View details →

snATAC-seq and snRNA-seq in the chromatin landscape of healthy and injured cell types in the human kidney

Isolated nuclei were immediately processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (v1.0) kit, following the step-by-step protocol provided online [https://dx.doi.org/10.17504/protocols.io.5qpvoby69l4o/v2]. The RNA and ATAC libraries were separately sequenced on the NovaSeq 6000 system (Illumina) using the NovaSeq Control Software versions 1.7.0 and 1.7.5. Sample demultiplexing, barcode processing, gene expression quantification, and open chromatin peak quantification were performed using the Cell Ranger Arc software (version 2.0.0) with the GRCh38 (hg38) reference genome.  Published in: DOI: <a href="https://doi.org/10.1038/s41467-023-44467-6" target="_blank" rel="noopener"> 10.1038/s41467-023-44467-6 </a>

opencc-by-4.0May 2023View details →

Inlists for SN 2018gj: A Short-plateau Type II Supernova with Persistent Blue-shifted H-alphaEmission

We present the MESA inlists  to generate models used in the research work "SN 2018gj: A Short-plateau Type II Supernova with Persistent Blue-shifted H-alpha Emission."

opencc-by-4.0Jun 2023View details →

Gene-based association analysis on 7 chronic pain types

Gene-based association testing was run GCTA-fastBAT package on 7 phenotypes: chronic back, neck, hip, knee, facial, and abdominal pain and chronic headache. The summary statistics used to produce the text files required for this analysis have also been uploaded.

opencc-zeroJun 2023View details →

Disease parameters following ocular herpes simplex virus type 1 infection are similar in male and female BALB/C mice

Sex-related differences in the incidence or severity of infection have been described for multiple viruses. With herpes simplex viruses, the best example is HSV-2 genital infection where women have a higher incidence of infection and can have more severe infections than men. HSV-1 causes several types of infections including skin and mucosal ulcers, keratitis, and encephalitis in humans that do not appear to have a strong biological sex component. Given that mouse strains differ in their MHC loci it is important to determine if sex differences occur in multiple strains of mice. Our goal was to answer two questions: Are virus-related sex differences present in BALB/C mice and does virulence of the viral strain have an effect? We generated a panel of recombinant HSV-1 viruses with differing virulence phenotypes and characterized multiple clinical correlates of ocular infection in BALB/c mice. We found no sex-specific differences in blepharitis, corneal clouding, neurovirulence, and viral titers in eye washes. Sex differences in neovascularization, weight loss, and eyewash titers were observed for some recombinants, but these were not consistent across the phenotypes tested for any recombinant virus. Considering these findings, we conclude that there are no significant sex-specific ocular pathologies in the parameters measured, regardless of the virulence phenotype following ocular infection in BALB/c mice, suggesting that the use of both sexes is not necessary for the bulk of ocular infection studies.

opencc-zeroJun 2023View details →

CMT1A-BioStampNPoint2023: Charcot-Marie-Tooth disease type 1A accelerometry dataset from three wearable sensor study

The CMT1A-BioStampNPoint2023 dataset provides data from a wearable sensor accelerometry study conducted for studying gait, balance, and activity in 15 individuals with Charcot-Marie-Tooth disease Type 1A (CMT1A). In addition to individuals with CMT1A, the dataset also includes data for 15 controls that also went through the same in-clinic study protocol as the CMT1A participants with a substantial fraction (9) of the controls also participating in the in-home study protocol. For the CMT1A participants, data is provided for 15 participants for the baseline visit and associated home recording duration and, additionally, for a subset of 12 of these participants data is also provided for a 12-month longitudinal visit and associated home recording duration. For controls, no longitudinal data is provided as none was recorded. The data were acquired using lightweight MC 10 BioStamp NPoint sensors (MC 10 Inc, Lexington, MA), three of which were attached to each participant for gathering data over a roughly one day interval. For additional details, see the description in the "README.md" included with the dataset.

opencc-by-4.0Jun 2023View details →

Volume of Interest: Exploring New Data Types in Urban Functional Zones

随着全球城镇化的发展,实现城市功能区的精细化识别已成为一项挑战。基于POI数据的传统方法不足以识别不同区域的功能特征。以往研究中基本单位设置不精确、POI重分类标准模糊、功能区定义模糊等局限性,成为获得准确识别结果的重大障碍。为了解决这些问题,本研究提出了一种将POI数据扩展到三维空间并生成VOI(感兴趣体积)数据的方法。以香港一个小区域为例,采用一系列指标量化功能特征,然后将识别结果与基于POI的方法进行比较。最终鉴定总体准确率和kappa系数分别达到85.67%和0.7619,表明基于VOI的方法与实际情况基本吻合。分析表明,VOI数据包含更丰富、更全面的城市空间信息,能够更好地反映城市内不同区域之间的联系和影响。本研究可为城市功能区深入研究提供参考案例。

opencc-by-4.0Dec 2022View details →

Dataset of H-alpha activity indices of F-, G-, and K-type stars observed by the LAMOST Medium-Resolution Spectroscopic Survey

This dataset of H-alpha activity indices is for investigation of stellar H-alpha chromospheric activity based on the LAMOST Medium-Resolution Spectroscopic Survey (MRS). High signal-to-noise ratio MRS coadded spectra of F-, G-, and K-type stars (4000-7000 K) from LAMOST Data Release 8 are utilized in the dataset (329,294 spectra in total). The H-alpha activity index (I_halpha) and the H-alpha R-index (R_halpha) are evaluated for the MRS spectra. The values of the H-alpha indices and their uncertainties, as well as the related spectroscopic parameters from the LAMOST catalogs, are stored in a CSV-format file (file name: Halpha_activity_indices_LAMOST_MRS_DR8.csv).   Columns included in the dataset: obsid - unique observation identifier of LAMOST MRS ra - right ascension of the observed object (unit: degree) dec - declination of the observed object (unit: degree) obsdate - UTC date of the observation (format: YYYY-MM-DD) fitsname - MRS FITS data file name sn_B - signal-to-noise ratio of the blue band of MRS sn_R - signal-to-noise ratio of the red band of MRS band_para - indicating which band of MRS is used by the LASP to determine the stellar atmospheric parameters; ‘B’ representing the blue band and ‘R’ representing the red band teff - effective temperature determined by the LASP (unit: K) teff_err - uncertainty of teff (unit: K) logg - surface gravity determined by the LASP (unit: dex) logg_err - uncertainty of logg (unit: dex) feh - metallicity determined by the LASP (unit: dex) feh_err - uncertainty of feh (unit: dex) rv_r0 - radial velocity determined based on the red band data of MRS (unit: km/s) rv_r0_err - uncertainty of rv_r0 (unit: km/s) category* - ‘main-sequence’ or ‘giant’ or ‘intermediate-zone’ I_halpha* - H-alpha activity index I_halpha_err* - uncertainty of I_halpha chi* - χ factor for calculating R_halpha from I_halpha (unit: 1/Å) chi_err* - uncertainty of chi (unit: 1/Å) R_halpha* - H-alpha R-index R_halpha_err* - uncertainty of R_halpha (Note: The columns marked with an asterisk are provided by this dataset. Other columns are from the catalogs of LAMOST DR8 v1.1. LASP is an acronym for the LAMOST Stellar Parameter Pipeline. A value of -9999.0 in the dataset indicates that it is not available.)

Data from: Chemically distinct particle phase emissions from highly controlled pyrolysis of three wood types

Wood pyrolysis is a distinct process that precedes combustion and contributes to biomass and biofuel burning gas phase and particle phase emissions. Pyrolysis is defined as the thermochemical degradation of wood, the products of which can be released directly or undergo further reaction during gas-phase combustion. To isolate and study the processes and emissions of pyrolysis, a custom-made reactor was used to uniformly heat small blocks of wood in a nitrogen atmosphere. Pieces of maple, Douglas fir and oak wood (maximum 155 cm3) were pyrolyzed in a temperature-controlled chamber set to 400, 500, or 600°C. Real time particle phase emissions were measured with a Soot Particle Aerosol Mass Spectrometer (SP-AMS) and correlated with simultaneous gas phase emission measurements of CO. Particle and gas emissions increased rapidly after inserting a wood sample, remained high for tens of minutes, and then dropped rapidly leaving behind char. The particulate mass loading profiles varied with elapsed experiment time, wood type and size, and pyrolysis chamber temperature. The chemical composition of the emitted particles was organic (C, H, O), with negligible black carbon or nitrogen. The emitted particles displayed chemical signatures unique to pyrolysis and notably different from flaming or smoldering wood combustion. The most abundant fragment ions in the mass spectrum were CO+ and CHO+, which together made up 23 % of the total aerosol mass on average, whereas CO2+ accounted for less than 4 %, in sharp contrast with ambient aerosol where CO2+ is often a dominant contributor. The mass spectra also showed signatures of levoglucosan and other anhydrous sugars. The fractional contribution of m/z 60, traditionally a tracer for anhydrous sugars including levoglucosan, to total loading (f60) was observed to be between 0.002 and 0.039, similar to previous observations from wild and controlled wood fires. Atomic ratios of oxygen and hydrogen to carbon, O : C and H : C as calculated from AMS mass spectra, varied between 0.41–0.81 and 1.06–1.57, respectively, with individual conditions lying within a continuum of O : C and H : C for wood's primary constituents: cellulose, hemicellulose, and lignin. This work identifies the mass spectral signatures of particle emissions directly from pyrolysis, including f60 and CO+/CO2+ ratio, through controlled laboratory experiments in order to help understand the importance of pyrolysis emissions in the broader context of wild and controlled wood fires.

Tn-seq wig files for wild-type and ΔrecG library replicates

Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli, the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing (Tn-seq) to identify recG genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the dam, uvrD, rnhA, radA, and rep genes. The conditional importance of these five genes in cells lacking recG was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with uvrD, rep, and radA; but not rnhA or dam) were suppressed by deletion of recF or recO, indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a recG deletion when combined with dam, uvrD, radA, or rnhA deletions but not with rep. The results reinforce the idea of RecG as a general genome guardian. Its varied genetic interactions reflect critical roles in several different repair contexts, where RecG alleviates toxic DNA intermediates.

Phenotype images of the developing heart from wild type and Sox7 mutant mouse embryo

The cardiac endothelium influences ventricular chamber development by coordinating trabeculation and compaction. However, the endothelial-specific molecular mechanisms mediating this coordination are not fully understood. Here, we identified the Sox7 transcription factor as a critical cue instructing cardiac endothelium identity during ventricular chamber development. Endothelial-specific loss of Sox7 function in mice results in cardiac ventricular defects similar to non-compaction cardiomyopathy, with a change in the proportions of trabecular and compact cardiomyocytes in the mutant hearts. This phenotype is paralleled by abnormal coronary artery formation. Loss of Sox7 function disrupts the transcriptional regulation of the Notch pathway and connexins 37 and 40, which govern coronary arterial specification. Upon Sox7 endothelial-specific deletion, single-nuclei transcriptomics analysis identified the depletion of a subset of Sox9/Gpc3 positive endocardial progenitor cells and an increase in erythro-myeloid cell lineages. Fate mapping analysis revealed that a subset of Sox7-null endothelial cells transdifferentiate into hematopoietic but not cardiomyocyte lineages. Our findings determine that Sox7 maintains cardiac endothelial cell identity, which is crucial to the cellular cross-talk that drives ventricular compaction and coronary artery development.

opencc-by-4.0Jul 2023View details →

Technical drawings for the production of dual-type temperature probes

Technical drawings for manufacturing prototypes of dual-type temperature probes that were used for testing the new concept of dual-type thermometers. Dual-type thermometers enable in-situ determination of thermocouple drift. The basic idea behind the concept is that thermocouple drift can be continuously monitored in situ by placing an additional and different temperature sensor in close proximity. The essential requirement for this additional sensor is that it experiences a drift that is lower than the drift of the monitored thermocouple. A drift of a thermocouple can be determined by an algorithm that monitors, and over time compares, the differences in its temperature readings and the readings of an additional (reference) sensor.

Excited state observation of active K-Ras reveals differential structural dynamics of wild-type versus oncogenic G12D and G12C mutants

Despite the prominent role of the K-Ras protein in many different types of human cancer, major gaps in atomic-level information severely limit our understanding of K-Ras function in health and disease. Here, we report the quantitative backbone structural dynamics of K-Ras by solution NMR spectroscopy of the active state of wild-type K-Ras·GTP and two of its oncogenic P-loop mutants, G12D and G12C, using a novel nanoparticle-assisted spin relaxation method, relaxation dispersion and chemical exchange saturation transfer experiments covering the entire range of timescales from picosecond to milliseconds. Our combined experiments allow the detection and analysis of the functionally critical Switch I and Switch II regions that have previously remained largely unobservable by X-ray crystallography and NMR spectroscopy. Our data reveal cooperative transitions of K-Ras·GTP to a highly dynamic excited state that closely resembles the partially disordered K-Ras·GDP state. These results advance our understanding of differential GTPase activities and signaling properties of the WT versus mutants and may thus guide new strategies for the development of therapeutics.